X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fgui%2FAnnotationColourChooser.java;h=7ed178b4bdde183a24ec7b9f71966ec35767d20f;hb=f2fed0286852eee53492661a16309f6948f7ce05;hp=384635b5dcbe2df56c25e5687d5c1896e8e3050a;hpb=cc0681e25e04081ff98072750ad7eb041dcf3d18;p=jalview.git

diff --git a/src/jalview/gui/AnnotationColourChooser.java b/src/jalview/gui/AnnotationColourChooser.java
index 384635b..7ed178b 100644
--- a/src/jalview/gui/AnnotationColourChooser.java
+++ b/src/jalview/gui/AnnotationColourChooser.java
@@ -53,8 +53,6 @@ import net.miginfocom.swing.MigLayout;
 @SuppressWarnings("serial")
 public class AnnotationColourChooser extends AnnotationRowFilter
 {
-  private static final int ONETHOUSAND = 1000;
-
   private ColourSchemeI oldcs;
 
   private JButton defColours;
@@ -147,7 +145,8 @@ public class AnnotationColourChooser extends AnnotationRowFilter
                 "error.implementation_error_dont_know_about_threshold_setting"));
       }
       thresholdIsMin.setSelected(acg.isThresholdIsMinMax());
-      thresholdValue.setText("" + acg.getAnnotationThreshold());
+      thresholdValue
+              .setText(String.valueOf(acg.getAnnotationThreshold()));
     }
 
     jbInit();
@@ -317,7 +316,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
   @Override
   public void reset()
   {
-    av.setGlobalColourScheme(oldcs);
+    this.ap.alignFrame.changeColour(oldcs);
     if (av.getAlignment().getGroups() != null)
     {
 
@@ -338,7 +337,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       {
         updateView();
       }
-      getCurrentAnnotation().threshold.value = slider.getValue() / 1000f;
+      getCurrentAnnotation().threshold.value = getSliderValue();
       propagateSeqAssociatedThreshold(updateAllAnnotation,
               getCurrentAnnotation());
       ap.paintAlignment(false, false);
@@ -378,6 +377,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
     thresholdValue.setEnabled(true);
     thresholdIsMin.setEnabled(!useOriginalColours.isSelected());
 
+    final AlignmentAnnotation currentAnnotation = getCurrentAnnotation();
     if (selectedThresholdItem == AnnotationColourGradient.NO_THRESHOLD)
     {
       slider.setEnabled(false);
@@ -386,33 +386,26 @@ public class AnnotationColourChooser extends AnnotationRowFilter
       thresholdIsMin.setEnabled(false);
     }
     else if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD
-            && getCurrentAnnotation().threshold == null)
+            && currentAnnotation.threshold == null)
     {
-      getCurrentAnnotation().setThreshold(new GraphLine(
-              (getCurrentAnnotation().graphMax
-                      - getCurrentAnnotation().graphMin) / 2f,
+      currentAnnotation.setThreshold(new GraphLine(
+              (currentAnnotation.graphMax - currentAnnotation.graphMin)
+                      / 2f,
               "Threshold", Color.black));
     }
 
     if (selectedThresholdItem != AnnotationColourGradient.NO_THRESHOLD)
     {
       adjusting = true;
-      float range = getCurrentAnnotation().graphMax * ONETHOUSAND
-              - getCurrentAnnotation().graphMin * ONETHOUSAND;
-
-      slider.setMinimum(
-              (int) (getCurrentAnnotation().graphMin * ONETHOUSAND));
-      slider.setMaximum(
-              (int) (getCurrentAnnotation().graphMax * ONETHOUSAND));
-      slider.setValue(
-              (int) (getCurrentAnnotation().threshold.value * ONETHOUSAND));
-      thresholdValue.setText(getCurrentAnnotation().threshold.value + "");
-      slider.setMajorTickSpacing((int) (range / 10f));
+      setSliderModel(currentAnnotation.graphMin, currentAnnotation.graphMax,
+              currentAnnotation.threshold.value);
       slider.setEnabled(true);
+
+      setThresholdValueText();
       thresholdValue.setEnabled(true);
       adjusting = false;
     }
-    colorAlignmentContaining(getCurrentAnnotation(), selectedThresholdItem);
+    colorAlignmentContaining(currentAnnotation, selectedThresholdItem);
 
     ap.alignmentChanged();
   }
@@ -442,7 +435,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
 
     acg.setThresholdIsMinMax(thresholdIsMin.isSelected());
 
-    av.setGlobalColourScheme(acg);
+    this.ap.alignFrame.changeColour(acg);
 
     if (av.getAlignment().getGroups() != null)
     {
@@ -454,7 +447,7 @@ public class AnnotationColourChooser extends AnnotationRowFilter
           continue;
         }
         sg.setColourScheme(
-                acg.getInstance(sg, ap.av.getHiddenRepSequences()));
+                acg.getInstance(av, sg));
       }
     }
   }
@@ -465,5 +458,4 @@ public class AnnotationColourChooser extends AnnotationRowFilter
     super.sliderDragReleased();
     ap.paintAlignment(true, true);
   }
-
 }